The main character is a girl named Karana, and that is her secret name. Wonapalei is her common name (everyone in the village has a secret name). Her people live in a village called Ghalas-at, gathering roots and fishing to supply the tribe. One day, a ship of Aleuts, led by a Russian named Captain Orlov, arrive and persuade the natives into letting them hunt sea otter in return for other goods. However, the Aleuts attempt to swindle the islanders and leave without paying. When they are confronted by Chief Chowig, Karana's father, a battle breaks out, and lives are lost on both sides. The tribe is decimated by the battle and the Aleuts leave the island, leaving little payment for the otters they hunted. Karana's father and many other men in the tribe die after the battle.

Later, the "replacement chief", Chief Kimki, leaves the island for new land in the east. Eventually, he is able to send a ship to bring his people to the mainland, even though he himself does not return. The white men came to Karana's village and told them to pack their goods and go to the ship. Karana's brother, Ramo left the ship to retrieve his fishing spear. Although Karana urges the captain to wait for her brother Ramo to return, the ship must leave before a storm approaches. Karana jumps off the ship and swims to shore, and the ship departs without them.

The siblings live alone on the island,hoping the ship will return. Ramo is eventually killed by a pack of feral dogs (some of the dogs joined the feral pack after the Aleuts killed their owners). Alone on the island, Karana must now take on traditionallymale tasks, such as hunting, making spears, or building canoes, in order to survive. She vows to avenge her brother's death and kills several of the dogs, but has a change of heart when she encounters the leader of the pack. She tames him and names him Rontu, meaning "fox eyes" in her language.

Over time, Karana makes a life for herself. She builds a home made of whale bones and even stocks a cave with provisions in case the Aleuts ever come back, so she can hide from them. As she explores her island, Karana discovers ancient artifacts and a large squid (which she calls a devilfish). As time passes, she decides to hunt the devilfish. She also tames some birds and an otter; she feels a close kinship to the animals, the only inhabitants of the island beside herself.

One summer, the Aleuts return, and Karana takes refuge in the cave. She observes the Aleuts closely, and soon realizes that there is a girl, Tutok, among the Aleuts who takes care of the domestic duties, including getting water from the pool near Karana's cave. Despite Karana's precautions, she and the young Aleut woman meet and befriend each other. They exchange presents with each other when possible. Karana realizes how lonely she has been without other people. Later the Aleuts leave, with Tutok; the men are none the wiser of Karana's presence, but their departure also deprives her of her newfound friend.

More time goes by, and Rontu dies. She soon finds a young dog that looks like Rontu and takes him in, naming him Rontu-Aru ("Son of Rontu"). One day, Karana sees the sails of a ship. It docks at the shore, but it then leaves. Two years later, in the spring, the boat comes back, so she dresses in her finest attire and goes to the shore to meet the boat. Her rescuers realize her attire will not be appropriate for the mainland, and they have a dress made for her. Although she does not like the dress, Karana realizes that this is part of her new life. The ship sails away, and takes Karana and Rontu-Aru to the mission in Santa Barbara, California.

The novel was highly acclaimed upon its publication, and became O'Dell's best known work. It was awarded the Newbery Medal in 1961.[1] O'Dell published a sequel, Zia, in 1976. This book follows 14-year-old Zia, Karana's niece, who believes her aunt is still alive, and eventually brings about her rescue by George Nidever.